Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants

• Published in: Clinical microbiology and infection Vol. 28; no. 1; pp. 124 - 129
• Main Authors: Mertens, Joachim, Coppens, Jasmine, Loens, Katherine, Le Mercier, Marie, Xavier, Basil Britto, Lammens, Christine, Vandamme, Sarah, Jansens, Hilde, Goossens, Herman, Matheeussen, Veerle
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.01.2022; European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd
• Subjects: Algorithms; Coronavirus disease 2019; COVID-19 - diagnosis; Humans; Melting curve analysis; Multiplex Polymerase Chain Reaction; Mutation; Nucleic acid testing; Original; Pandemics; Polymerase Chain Reaction; Polymorphism, Single Nucleotide; SARS-CoV-2 - genetics; Severe acute respiratory syndrome coronavirus 2; Severe acute respiratory syndrome coronavirus 2 variants; Spike Glycoprotein, Coronavirus - genetics; Testing algorithm; Whole-genome sequencing; Polymerase chain reaction; Severe acute respiratory syndrome coronavirus 2; Severe acute respiratory syndrome coronavirus 2 variants; Testing algorithm; Coronavirus disease 2019; Nucleic acid testing; Whole-genome sequencing; Melting curve analysis
• ISSN: 1198-743X; 1469-0691; 1469-0691
• DOI: 10.1016/j.cmi.2021.09.007

To evaluate a testing algorithm for the rapid identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that includes the use of PCR-based targeted single nucleotide polymorphism (SNP) detection assays preceded by a multiplex PCR sensitive to S-Gene Target Failure (SGTF). PCR SNP assays targeting SARS-CoV-2 S-gene mutations ΔH69–V70, L452R, E484K, N501Y, H655Y and P681R using melting curve analysis were performed on 567 samples in which SARS-CoV-2 viral RNA was detected by a multiplex PCR. Viral whole-genome sequencing (WGS) was performed to confirm the presence of SNPs and to identify the Pangolin lineage. Additionally, 1133 SARS-CoV-2 positive samples with SGTF were further assessed by WGS to determine the presence of ΔH69–V70. The N501Y-specific assay (n = 567) had an overall percentage agreement (OPA) of 98.5%. The ΔH69-V70-specific (n = 178) and E484K-specific (n = 401) assays had OPA of 96.6% and 99.7%, respectively. Assessment of H655Y (n = 139) yielded a 100.0% concordance when applied in the proposed algorithm. The L452R-specific (n = 67) and P681R-specific (n = 62) assays had an OPA of 98.2% and 98.1%, respectively. The proposed algorithm identified six variants of concern/interest (VOC/VOI)—Alpha (n = 149), Beta (n = 65), Gamma (n = 86), Delta (n = 49), Eta (n = 6), Kappa (n = 6)—and 205 non-VOC/VOI strains—including the variants under monitoring B.1.214.2 (n = 43) and B.1.1.318 (n = 18) and Epsilon (n = 1). An excellent concordance was observed for the identification of all SARS-CoV-2 lineages evaluated. We present a flexible testing algorithm for the rapid detection of current and emerging SARS-CoV-2 VOC/VOIs, which can be easily adapted based on the local endemicity of specific variants.